Thank you very much for your wonderful Prokka, I used it to annotation my bacteria before, now I would like to use it on my metatranscriptome virus.
(1) Is it OK I just use the parameter –kingdom Viruses –metagenome ? You said that Prokka couldn’t annotate the polyprotein, I will use prokka annotate firstly, and plus VADR to do further annotation on specific protein (mature peptide of polyprotein), is it OK? Or any other advice would be appreciated.
(2) May I know what’s the virus related database Prokka included default, from Refseq or Uniport or others, and how many sequences and when do you collected them?
@tseemann Hi Torsten Seemann,
Thank you very much for your wonderful Prokka, I used it to annotation my bacteria before, now I would like to use it on my metatranscriptome virus. (1) Is it OK I just use the parameter –kingdom Viruses –metagenome ? You said that Prokka couldn’t annotate the polyprotein, I will use prokka annotate firstly, and plus VADR to do further annotation on specific protein (mature peptide of polyprotein), is it OK? Or any other advice would be appreciated. (2) May I know what’s the virus related database Prokka included default, from Refseq or Uniport or others, and how many sequences and when do you collected them?
Thanks in advance.